Today we noticed "missing layers" in some ArcGIS Server 10.4.1 map services and found that the SQL Server windows services for our enterprise geodatabase that are set to start automatically did not start after a maintenance reboot last night.
Starting the windows services manually works fine but some of the GIS map services were still only showing partial list of layers.
Those SQL services are now changed from Automatic to Automatic (Delayed Start)
I think they used to be set to Automatic (Delayed Start) but a recent SQL Server back in November to update from SQL 2008 R2 to SQL 2014 to get compliant with ArcGIS 10.4.1 probably set them back to default of just Automatic.
We hadn't rebooted the SQL Server during the holidays until a couple weeks ago and thought the services not auto-starting was just a fluke.
We'll see if the Automatic (Delayed Start) works during the next maintenance window.
The troubleshooting led us to this Microsoft Bug: 59557
It seems because our servers are now virtual on fast SSD drives, they boot too fast for service domain #user accounts to get authenticated.
This Microsoft article outlines a work-around registry edit we can also try.